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NIFTI_NORDIC.m
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NIFTI_NORDIC.m
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function NIFTI_NORDIC(fn_magn_in,fn_phase_in,fn_out,ARG)
% fMRI
% fn_magn_in='name.nii.gz';
% fn_phase_in='name2.nii.gz';
% fn_out=['NORDIC_' fn_magn_in(1:end-7)];
% ARG.temporal_phase=1;
% ARG.phase_filter_width=10;
% NIFTI_NORDIC(fn_magn_in,fn_phase_in,fn_out,ARG)
%
% dMRI
% fn_magn_in='name.nii.gz';
% fn_phase_in='name2.nii.gz';
% fn_out=['NORDIC_' fn_magn_in(1:end-7)];
% ARG.temporal_phase=3;
% ARG.phase_filter_width=3;
% NIFTI_NORDIC(fn_magn_in,fn_phase_in,fn_out,ARG)
%
%
% file_input assumes 4D data
%
%OPTIONS
% ARG.DIROUT VAL= string Default is empty
% ARG.noise_volume_last VAL = num specifiec volume from the end of the series
% 0 default
%
% ARG.factor_error val = num >1 use higher noisefloor <1 use lower noisefloor
% 1 default
%
% ARG.full_dynamic_range val = [ 0 1] 0 keep the input scale, output maximizes range.
% Default 0
% ARG.temporal_phase val = [1 2 3] 1 was default, 3 now in dMRI due tophase errors in some data
% ARG.NORDIC val = [0 1] 1 Default
% ARG.MP val = [0 1 2] 1 NORDIC gfactor with MP estimation.
% 2 MP without gfactor correction
% 0 default
% ARG.kernel_size_gfactor val = [val1 val2 val], defautl is [14 14 1]
% ARG.kernel_size_PCA val = [val1 val2 val], default is val1=val2=val3;
% ratio of 11:1 between spatial and temproal voxels
% ARG.magnitude_only val =[] or 1. Using complex or magntiude only. Default is []
% Function still needs two inputs but will ignore the second
%
% ARG.save_add_info val =[0 1]; If it is 1, then an additonal matlab file is being saved with degress removed etc.
% default is 0
% ARG.make_complex_nii if the field exist, then the phase is being saved in a similar format as the input phase
%
% ARG.phase_slice_average_for_kspace_centering val = [0 1]
% if val =0, not used, if val=1 the series average pr slice is first removed
% default is now 0
% ARG.phase_filter_width val = [1... 10] Specifiec the width of the smoothing filter for the phase
% default is now 3
%
% ARG.save_gfactor_map val = [1 2]. 1, saves the RELATIVE gfactor, 2 saves the
% gfactor and does not complete the NORDIC processing
% ARG.write_gzipped_niftis val = [0, 1] Output files are written to
% disk ask compressed *.nii.gz NIfTIs.
% default is 0 (= false).
% TODO
% Scaling relative to the width of the MP spectrum, if one wants to be
% conservative
%
% 4/15/21 swapped the uint16 and in16 for the phase
%
% VERSION 4/22/2021
% Copyright Board of Regents, University of Minnesota, 2022
if ~exist('ARG') % initialize ARG structure
ARG.DIROUT=[pwd '/'];
elseif ~isfield(ARG,'DIROUT') % Specify where to save data
ARG.DIROUT=[pwd '/'];
end
if ~isfield(ARG,'noise_volume_last')
ARG.noise_volume_last=0; % there is no noise volume {0 1 2 ...}
end
if ~isfield(ARG,'factor_error')
ARG.factor_error=1.0; % error in gfactor estimatetion. >1 use higher noisefloor <1 use lower noisefloor
end
if ~isfield(ARG,'full_dynamic_range')
ARG.full_dynamic_range=0; % Format o
end
if ~isfield(ARG,'temporal_phase')
ARG.temporal_phase=1; % Correction for slice and time-specific phase
end
if ~isfield(ARG,'NORDIC') & ~isfield(ARG,'MP')
ARG.NORDIC=1; % threshold based on Noise
ARG.MP=0; % threshold based on Marchencko-Pastur
elseif ~isfield(ARG,'NORDIC') % MP selected
if ARG.MP==1
ARG.NORDIC=0;
else
ARG.NORDIC=1;
end
elseif ~isfield(ARG,'MP') % NORDIC selected
if ARG.NORDIC==1
ARG.MP=0;
else
ARG.MP=1;
end
end
if ~isfield(ARG,'phase_filter_width')
ARG.phase_filter_width=3; % default is [14 14 90]
end
if ~isfield(ARG,'NORDIC_patch_overlap')
ARG.NORDIC_patch_overlap=2; % default is [14 14 90]
end
if ~isfield(ARG,'gfactor_patch_overlap')
ARG.gfactor_patch_overlap=2; % default is [14 14 90]
end
if ~isfield(ARG,'kernel_size_gfactor')
ARG.kernel_size_gfactor=[]; % default is [14 14 90]
end
if ~isfield(ARG,'kernel_size_PCA')
ARG.kernel_size_PCA=[]; % default is 11:1 ratio
end
if ~isfield(ARG,'phase_slice_average_for_kspace_centering');
ARG.phase_slice_average_for_kspace_centering=0;
end
if ~isfield(ARG,'magnitude_only') % if legacy data
ARG.magnitude_only=0; %
end
if isfield(ARG,'save_add_info'); end % additional information is saved in matlab file
if isfield(ARG,'make_complex_nii'); end % two output NII files are saved
if ~isfield(ARG,'save_gfactor_map') % save out a map of a relative gfactor
ARG.save_gfactor_map=[]; %
end
if isfield(ARG,'use_generic_NII_read') % save out a map of a relative gfactor
if ARG.use_generic_NII_read==1
path(path,'/home/range6-raid1/moeller/matlab/ADD/NIFTI/');
end
else
ARG.use_generic_NII_read=0;
end
if ~isfield(ARG,'data_has_zero_elements') %
ARG.data_has_zero_elements=0; % % If there are pixels that are constant zero
end
if ~isfield(ARG, 'write_gzipped_niftis')
ARG.write_gzipped_niftis = 0;
end
ARG;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ARG.magnitude_only~=1
try
info_phase=niftiinfo(fn_phase_in);
info=niftiinfo(fn_magn_in);
catch; disp('The niftiinfo fails at reading the header') ;end
if ARG.use_generic_NII_read~=1
I_M=abs(single(niftiread(fn_magn_in)));
I_P=single(niftiread(fn_phase_in));
else
try
tmp=load_nii(fn_magn_in);
I_M=abs(single(tmp.img));
tmp=load_nii(fn_phase_in);
I_P=single(tmp.img);
catch
disp('Missing nfiti tool. Serach mathworks for load_nii fileexchange 8797')
end
end
phase_range=single(max(I_P(:)));
phase_range_min=single(min(I_P(:)));
if ~exist('info_phase')
info_phase.Datatype=class(I_P);
info.Datatype=class(I_M);
end
% Here, we combine magnitude and phase data into complex form
fprintf('Phase should be -pi to pi...\n')
% convert to single and then scale the phase
I_P = single(I_P);
range_norm=phase_range-phase_range_min;
range_center=(phase_range+phase_range_min)/range_norm*1/2;
I_P = (single(I_P)./range_norm -range_center)*2*pi;
II=single(I_M) .* exp(1i*I_P);
if 0
if strmatch(info_phase.Datatype,'uint16')
I_P = single(I_P)/phase_range*2*pi;
II=single(I_M) .* exp(1i*I_P);
elseif strmatch(info_phase.Datatype,'int16')
I_P = (single(I_P)+1-(phase_range+1)/2)/(phase_range+1)*2*pi;
II=single(I_M) .* exp(1i*I_P);
elseif strmatch(info_phase.Datatype,'single')
phase_range_min=min(I_P(:));
range_norm=phase_range-phase_range_min;
range_center=(phase_range+phase_range_min)/range_norm*1/2;
I_P = (single(I_P)./range_norm -range_center)*2*pi;
II=single(I_M) .* exp(1i*I_P);
end
end
fprintf('Phase data range is %.2f to %.2f\n', min(I_P(:)), max(I_P(:)))
else
try
info=niftiinfo(fn_magn_in);
catch; disp('The niftiinfo fails at reading the header') ;end
if ARG.use_generic_NII_read~=1
I_M=abs(single(niftiread(fn_magn_in)));
else
tmp=load_nii(fn_magn_in);
I_M=abs(single(tmp.img));
end
if ~exist('info_phase')
info.Datatype=class(I_M);
end
end
if ~isempty(ARG.magnitude_only)
if ARG.magnitude_only==1
II=single(I_M);
ARG.temporal_phase=0;
end
end
TEMPVOL=abs(II(:,:,:,1));
ARG.ABSOLUTE_SCALE=min(TEMPVOL(TEMPVOL~=0));
II=II./ARG.ABSOLUTE_SCALE;
% load test_DATA
% II=II(:,:,:,1:95);
if size(II,4)<6
disp('Too few volumes')
% return
end
KSP2=II;
matdim=size(KSP2);
tt=mean(reshape(abs(KSP2),[],size(KSP2,4)));
[idx]=find(tt>0.95*max(tt));
meanphase=mean(KSP2(:,:,:,idx(1)),4);
if 1
disp('estimating slice-dependent phases ...')
meanphase=mean(KSP2(:,:,:,[1:end-ARG.noise_volume_last]),4);
for nsl=1:size(meanphase,3);
%meanphase2(:,:,nsl)=complex( medfilt2(squeeze(real(meanphase(:,:,nsl))),[7 7]), medfilt2(squeeze(imag(meanphase(:,:,nsl))),[7 7]) );
end
meanphase=meanphase*ARG.phase_slice_average_for_kspace_centering;
end
for slice=matdim(3):-1:1
for n=1:size(KSP2,4); % include the noise
KKSP2(:,:,slice,n)=KSP2(:,:,slice,n).*exp(-i*angle(meanphase(:,:,slice)));
end
end
DD_phase=0*KSP2;
if ARG.temporal_phase>0; % Standarad low-pass filtered map
for slice=matdim(3):-1:1
for n=1:size(KSP2,4);
tmp=KSP2(:,:,slice,n);
for ndim=[1:2]; tmp=ifftshift(ifft(ifftshift( tmp ,ndim),[],ndim),ndim+0); end
[nx, ny, nc, nb] = size(tmp(:,:,:,:,1,1));
tmp = bsxfun(@times,tmp,reshape(tukeywin(ny,1).^ARG.phase_filter_width,[1 ny]));
tmp = bsxfun(@times,tmp,reshape(tukeywin(nx,1).^ARG.phase_filter_width,[nx 1]));
for ndim=[1:2]; tmp=fftshift(fft(fftshift( tmp ,ndim),[],ndim),ndim+0); end
DD_phase(:,:,slice,n)=tmp;
end
end
end
if ARG.temporal_phase==2; % Secondary step for filtered phase with residual spikes
for slice=matdim(3):-1:1
for n=1:size(KSP2,4);
phase_diff=angle(KSP2(:,:,slice,n)./DD_phase(:,:,slice,n));
mask=abs(phase_diff)>1;
DD_phase2=DD_phase(:,:,slice,n);
tmp=(KSP2(:,:,slice,n));
DD_phase2(mask)= tmp(mask);
DD_phase(:,:,slice,n)=DD_phase2;
end
end
end
for slice=matdim(3):-1:1
for n=1:size(KSP2,4);
KSP2(:,:,slice,n)= KSP2(:,:,slice,n).*exp(-i*angle( DD_phase(:,:,slice,n) ));
end
end
disp('Completed estimating slice-dependent phases ...')
if isfield(ARG,'use_magn_for_gfactor')
if isempty(ARG.kernel_size_gfactor) | size(ARG.kernel_size_gfactor,2)<3
KSP2=abs(KSP2(:,:,1:end,1:min(90,end),1)); % should be at least 30 volumes
else
KSP2=abs(KSP2(:,:,1:end,1:min(ARG.kernel_size_gfactor(3),end),1));
end
else
if (isempty(ARG.kernel_size_gfactor) | size(ARG.kernel_size_gfactor,2)<3)
KSP2=(KSP2(:,:,1:end,1:min(90,end),1)); % should be at least 30 volumes
else
% KSP2=(KSP2(:,:,1:end,1:min(ARG.kernel_size_gfactor(3),end),1));
KSP2=(KSP2(:,:,1:end,1:min(ARG.kernel_size_gfactor(4),end),1));
end
end
KSP2(isnan(KSP2))=0;
KSP2(isinf(KSP2))=0;
master_fast=1;
KSP_recon=0*KSP2;
if isempty(ARG.kernel_size_gfactor)
ARG.kernel_size=[14 14 1];
else
ARG.kernel_size=[ARG.kernel_size_gfactor(1) ARG.kernel_size_gfactor(2) 1];
ARG.kernel_size=[ARG.kernel_size_gfactor(1) ARG.kernel_size_gfactor(2) ARG.kernel_size_gfactor(3)];
end
QQ.KSP_processed=zeros(1,size(KSP2,1)-ARG.kernel_size(1));
ARG.patch_average=0;
ARG.patch_average_sub= ARG.gfactor_patch_overlap;
ARG.LLR_scale=0;
ARG.NVR_threshold=1;
ARG.soft_thrs=10; % MPPCa (When Noise varies)
%ARG.soft_thrs=[]; % NORDIC (When noise is flat)
KSP_weight=KSP2(:,:,:,1)*0;
NOISE=KSP_weight;
Component_threshold=KSP_weight;
energy_removed=KSP_weight;
SNR_weight=KSP_weight;
QQ.KSP_processed=zeros(1,size(KSP2,1)-ARG.kernel_size(1));
if ARG.patch_average==0
KSP_processed=QQ.KSP_processed*0;
for nw1=2:max(1,floor(ARG.kernel_size(1)/ARG.patch_average_sub));
KSP_processed(1,nw1 : max(1,floor(ARG.kernel_size(1)/ARG.patch_average_sub)):end)=2;
end
KSP_processed(end)=0; % disp
QQ.KSP_processed=KSP_processed;
end
KSP_processed;
disp('estimating g-factor ...')
QQ.ARG=ARG;
for n1=1:size(QQ.KSP_processed,2)
% fprintf( [num2str(n1) ' '])
[KSP_recon,~,KSP_weight,NOISE,Component_threshold,energy_removed,SNR_weight]=sub_LLR_Processing(KSP_recon,KSP2,ARG,n1,QQ,master_fast,KSP_weight,NOISE,Component_threshold,energy_removed,SNR_weight) ; % save all files
% fprintf( [num2str(n1) ' '])
% if mod(n1,20)==0; disp(' ');end
end
KSP_recon=KSP_recon./repmat((KSP_weight),[1 1 1 size(KSP2,4)]);
ARG.NOISE= sqrt(NOISE./KSP_weight);
ARG.Component_threshold = Component_threshold./KSP_weight;
ARG.energy_removed = energy_removed./KSP_weight;
ARG.SNR_weight = SNR_weight./KSP_weight;
IMG2=KSP_recon;
ARG2=ARG;
disp('completed estimating g-factor')
gfactor=ARG.NOISE;
if size(KSP2,4)<6; % gfactor stimation most likely failed, replace with median estimated
gfactor(isnan(gfactor))=0;
gfactor(gfactor==0)=median(gfactor(gfactor~=0));
end
if sum(gfactor(:)==0)>0; % gfactor stimation most likely failed since it is zero
gfactor(isnan(gfactor))=0;
gfactor(gfactor<1)=median(gfactor(gfactor~=0));
ARG.data_has_zero_elements=1;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ARG.MP==2;
gfactor=ones(size(gfactor));
end
% gfactor=ones(size(gfactor));
if ( ARG.save_gfactor_map==2 ) | ( ARG.save_gfactor_map==1 )
g_IMG=abs(gfactor(:,:,:,1:end)); % remove g-factor and noise for DUAL 1
g_IMG(isnan(g_IMG))=0;
tmp=sort(abs(g_IMG(:))); sn_scale=2*tmp(round(0.99*end));%sn_scale=max();
gain_level=floor(log2(32000/sn_scale));
if ARG.full_dynamic_range==0; gain_level=0;end
if strmatch(info.Datatype,'uint16')
g_IMG= uint16(abs(g_IMG)*2^gain_level);
elseif strmatch(info.Datatype,'int16')
g_IMG= int16(abs(g_IMG)*2^gain_level);
else
g_IMG= single(abs(g_IMG)*2^gain_level);
end
niftiwrite((g_IMG),[ARG.DIROUT 'gfactor_' fn_out(1:end) '.nii'], ...
'Compressed', ARG.write_gzipped_niftis)
if ARG.save_gfactor_map==2
return
end
end
KSP2=II;
matdim=size(KSP2);
for slice=matdim(3):-1:1
for n=1:size(KSP2,4); % include the noise
KSP2(:,:,slice,n)=KSP2(:,:,slice,n).*exp(-i*angle(meanphase(:,:,slice)));
end
end
for n=1:size(KSP2,4);
KSP2(:,:,:,n)= KSP2(:,:,:,n)./ gfactor;
end
if ARG.noise_volume_last>0
KSP2_NOISE =KSP2(:,:,:,end+1-ARG.noise_volume_last);
end
if ARG.temporal_phase==3; % Secondary step for filtered phase with residual spikes
for slice=matdim(3):-1:1
for n=1:size(KSP2,4);
phase_diff=angle(KSP2(:,:,slice,n)./DD_phase(:,:,slice,n));
mask = abs(phase_diff)>1;
mask2 = abs(KSP2(:,:,slice,n))>sqrt(2);
DD_phase2=DD_phase(:,:,slice,n);
tmp=(KSP2(:,:,slice,n));
DD_phase2(mask.*mask2==1)= tmp(mask.*mask2==1);
DD_phase(:,:,slice,n)=DD_phase2;
end
end
end
for slice=matdim(3):-1:1
for n=1:size(KSP2,4);
KSP2(:,:,slice,n)= KSP2(:,:,slice,n).*exp(-i*angle( DD_phase(:,:,slice,n) ));
end
end
KSP2(isnan(KSP2))=0;
KSP2(isinf(KSP2))=0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ARG.noise_volume_last>0
%tmp_noise=KSP2(:,:,:,end+1-ARG.noise_volume_last);
tmp_noise=KSP2_NOISE;
tmp_noise(isnan(tmp_noise))=0;
tmp_noise(isinf(tmp_noise))=0;
ARG.measured_noise=std(tmp_noise(tmp_noise~=0)); % sqrt(2) for real and complex
else
ARG.measured_noise=1; % IF COMPLEX DATA
end
if ~isfield(ARG,'use_magn_for_gfactor') & (isempty(ARG.magnitude_only) | ARG.magnitude_only==0) %% WOULD THIS BE THE ISSUE & replaced by |
ARG.measured_noise = ARG.measured_noise/sqrt(2)
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ARG.data_has_zero_elements==1
MASK=(sum(abs(KSP2),4)==0);
Num_zero_elements=sum(MASK(:));
for nvol=1:size(KSP2,4)
tmp=KSP2(:,:,:,nvol);
tmp(MASK)=(randn(Num_zero_elements,1)+1i*randn(Num_zero_elements,1))/sqrt(2);
KSP2(:,:,:,nvol)=tmp;
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for readout=1:size(KSP2,1)
TT(readout)= std(reshape(KSP2(readout,:,:,:),[],1));
TT1(readout)= mean(reshape(KSP2(readout,:,:,:),[],1));
end
% ARG.measured_noise=median(TT([2:8 end-8:end-1]))
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
master_fast=1;
KSP_recon=0*KSP2;
ARG.kernel_size=repmat([ round((size(KSP2,4)*11)^(1/3)) ],1,3);
if isempty(ARG.kernel_size_PCA)
ARG.kernel_size=repmat([ round((size(KSP2,4)*11)^(1/3)) ],1,3);
else
ARG.kernel_size = ARG.kernel_size_PCA ;
end
if matdim(3) <= ARG.kernel_size(3) % Number of slices is less than cubic kernel
ARG.kernel_size = repmat([ round((size(KSP2,4)*11/matdim(3) )^(1/2)) ],1,2);
ARG.kernel_size(3)= matdim(3);
end
QQ.KSP_processed=zeros(1,size(KSP2,1)-ARG.kernel_size(1));
ARG.patch_average=0;
ARG.patch_average_sub= ARG.NORDIC_patch_overlap ;
% ARG.kernel_size=[7 7 7]; ARG.patch_average_sub=7; MPPCA
% ARG.soft_thrs=10; % MPPCa (When Noise varies)
ARG.LLR_scale=1;
ARG.NVR_threshold=0;
ARG.soft_thrs=[]; % NORDIC (When noise is flat)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
ARG.NVR_threshold=0;
for ntmp=1:10
[~,S,~]=svd(randn(prod(ARG.kernel_size),size(KSP2,4)));
ARG.NVR_threshold=ARG.NVR_threshold+S(1,1);
end
if ARG.magnitude_only~=1 % 4/29/2021
ARG.NVR_threshold= ARG.NVR_threshold/10*sqrt(2)* ARG.measured_noise*ARG.factor_error; % sqrt(2) due to complex 1.20 due to understimate of g-factor
else
ARG.NVR_threshold= ARG.NVR_threshold/10*ARG.measured_noise*ARG.factor_error; % sqrt(2) due to complex 1.20 due to understimate of g-factor
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ARG.MP>0
ARG.soft_thrs=10;
end
if isfield(ARG,'soft_thrs_in')
ARG.soft_thrs=ARG.soft_thrs_in;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
KSP_weight=KSP2(:,:,:,1)*0;
NOISE=KSP_weight;
Component_threshold=KSP_weight;
energy_removed=KSP_weight;
SNR_weight=KSP_weight;
QQ.KSP_processed=zeros(1,size(KSP2,1)-ARG.kernel_size(1));
if ARG.patch_average==0
KSP_processed=QQ.KSP_processed*0;
for nw1=2:max(1,floor(ARG.kernel_size(1)/ARG.patch_average_sub));
KSP_processed(1,nw1 : max(1,floor(ARG.kernel_size(1)/ARG.patch_average_sub)):end)=2;
end
KSP_processed(end)=0; % disp
QQ.KSP_processed=KSP_processed;
end
disp('starting NORDIC ...')
KSP_processed;
QQ.ARG=ARG;
for n1=1:size(QQ.KSP_processed,2)
[KSP_recon,~,KSP_weight,NOISE,Component_threshold,energy_removed,SNR_weight]=sub_LLR_Processing(KSP_recon,KSP2,ARG,n1,QQ,master_fast,KSP_weight,NOISE,Component_threshold,energy_removed,SNR_weight) ; % save all files
end
KSP_recon=KSP_recon./repmat((KSP_weight),[1 1 1 size(KSP2,4)]); % Assumes that the combination is with N instead of sqrt(N). Works for NVR not MPPCA
ARG.NOISE= sqrt(NOISE./KSP_weight);
ARG.Component_threshold = Component_threshold./KSP_weight;
ARG.energy_removed = energy_removed./KSP_weight;
ARG.SNR_weight = SNR_weight./KSP_weight;
IMG2=KSP_recon;
disp('completing NORDIC ...')
if isfield(ARG,'save_residual_matlab')
if ARG.save_residual_matlab==1;
Residual=KSP2-KSP_recon;
save(fullfile(ARG.DIROUT, ['RESIDUAL' fn_out '.mat']),'Residual','-v7.3')
end
end
for n=1:size(IMG2,4);
IMG2(:,:,:,n)= IMG2(:,:,:,n).* gfactor;
end
for slice=matdim(3):-1:1
for n=1:size(IMG2,4); % include the noise
IMG2(:,:,slice,n)=IMG2(:,:,slice,n).*exp(i*angle(meanphase(:,:,slice)));
end
end
for slice=matdim(3):-1:1
for n=1:size(IMG2,4);
IMG2(:,:,slice,n)= IMG2(:,:,slice,n).*exp(i*angle( DD_phase(:,:,slice,n) ));
end
end
IMG2=IMG2.*ARG.ABSOLUTE_SCALE;
IMG2(isnan(IMG2))=0;
if isfield(ARG,'make_complex_nii')
IMG2_tmp=abs(IMG2(:,:,:,1:end)); % remove g-factor and noise for DUAL 1
IMG2_tmp(isnan(IMG2_tmp))=0;
tmp=sort(abs(IMG2_tmp(:))); sn_scale=2*tmp(round(0.99*end));%sn_scale=max();
gain_level=floor(log2(32000/sn_scale));
%IMG2_tmp= int16(abs(IMG2_tmp)*2^gain_level);
if ARG.full_dynamic_range==0; gain_level=0;end
if strmatch(info.Datatype,'uint16')
IMG2_tmp= uint16(abs(IMG2_tmp)*2^gain_level);
elseif strmatch(info.Datatype,'int16')
IMG2_tmp= int16(abs(IMG2_tmp)*2^gain_level);
else
IMG2_tmp= single(abs(IMG2_tmp)*2^gain_level);
end
niftiwrite((IMG2_tmp),[ARG.DIROUT fn_out 'magn.nii'],info, ...
'Compressed', ARG.write_gzipped_niftis)
IMG2_tmp=angle(IMG2(:,:,:,1:end));
if strmatch(info_phase.Datatype,'int16')
% IMG2_tmp=IMG2_tmp+pi;
end
IMG2_tmp= (IMG2_tmp/(2*pi)+range_center)*range_norm;
if strmatch(info_phase.Datatype,'uint16')
IMG2_tmp= uint16(IMG2_tmp);
elseif strmatch(info_phase.Datatype,'int16')
IMG2_tmp= int16(IMG2_tmp);
else
IMG2_tmp= single((IMG2_tmp));
end
if 0
if strmatch(info_phase.Datatype,'uint16')
IMG2_tmp=IMG2_tmp/(2*pi)*phase_range;
IMG2_tmp= uint16(abs(IMG2_tmp)*2^gain_level);
elseif strmatch(info_phase.Datatype,'int16')
IMG2_tmp=IMG2_tmp/(2*pi)*phase_range;
IMG2_tmp= int16((IMG2_tmp)*2^gain_level);
else
IMG2_tmp= single(abs(IMG2_tmp)*2^gain_level);
end
end
niftiwrite((IMG2_tmp),[ARG.DIROUT fn_out 'phase.nii'],info_phase, ...
'Compressed', ARG.write_gzipped_niftis)
else
IMG2=abs(IMG2(:,:,:,1:end)); % remove g-factor and noise for DUAL 1
IMG2(isnan(IMG2))=0;
tmp=sort(abs(IMG2(:))); sn_scale=2*tmp(round(0.99*end));%sn_scale=max();
gain_level=floor(log2(32000/sn_scale));
if ARG.full_dynamic_range==0; gain_level=0;end
if strmatch(info.Datatype,'uint16')
IMG2= uint16(abs(IMG2)*2^gain_level);
elseif strmatch(info.Datatype,'int16')
IMG2= int16(abs(IMG2)*2^gain_level);
else
IMG2= single(abs(IMG2)*2^gain_level);
end
if ARG.use_generic_NII_read==0;
niftiwrite((IMG2),[ARG.DIROUT fn_out(1:end) '.nii'],info, ...
'Compressed', ARG.write_gzipped_niftis)
else
nii=make_nii(IMG2);
save_nii(nii, fullfile(ARG.DIROUT, [fn_out(1:end) '.nii']))
end
end
if isfield(ARG,'save_add_info')
if ARG.save_add_info==1
disp('saving additional info')
save(fullfile(ARG.DIROUT, [fn_out '.mat']),'ARG2','ARG','-v7.3')
end
end
return
function [KSP_recon,KSP2,KSP2_weight,NOISE, Component_threshold,energy_removed,SNR_weight]=sub_LLR_Processing(KSP_recon,KSP2,ARG,n1,QQ,master,KSP2_weight,NOISE,Component_threshold,energy_removed,SNR_weight)
if ~exist('NOISE'); NOISE=[]; end
if ~exist('Component_threshold');Component_threshold=[]; end
if ~exist('energy_removed'); energy_removed=[]; end
if ~exist('SNR_weight'); SNR_weight=[]; end
% QQ.KSP_processed 0 nothing done, 1 running, 2 saved 3 completed and averaged
if master==0 && ARG.patch_average==0
OPTION='NO_master_NO_PA';
elseif master==0 && ARG.patch_average==1
OPTION='NO_master_PA' ;
elseif master==1 && ARG.patch_average==0
OPTION='master_NO_PA' ;
elseif master==1 && ARG.patch_average==1
OPTION='master_PA' ;
end
switch OPTION
case 'NO_master_NO_PA'
case 'NO_master_PA'
case 'master_NO_PA'
case 'master_PA'
end
if QQ.KSP_processed(1,n1)~=1 && QQ.KSP_processed(1,n1)~=3 % not being processed also not completed yet
if QQ.KSP_processed(1,n1)==2 && master==1% processed but not added.
% loading instead of processing
% load file as soon as save, if more than 10 sec, just do the recon
% instead.
try % try to load otherwise go to next slice
load([ARG.filename 'slice' num2str(n1) '.mat'],'DATA_full2')
catch;
QQ.KSP_processed(1,n1)=0; % identified as bad file and being identified for reprocessing
return ;end
end
if QQ.KSP_processed(1,n1)~=2
QQ.KSP_processed(1,n1)=1; % block for other processes
if ~exist('DATA_full2')
ARG2=QQ.ARG;
if master==0
QQ.KSP_processed(1,n1)=1 ; % STARTING
KSP2a=QQ.KSP2([1:ARG.kernel_size(1)]+(n1-1),:,:,:); lambda=ARG2.LLR_scale*ARG.NVR_threshold;
else
QQ.KSP_processed(1,n1)=1 ; % STARTING
KSP2a=KSP2([1:ARG.kernel_size(1)]+(n1-1),:,:,:); lambda=ARG2.LLR_scale*ARG.NVR_threshold;
end
if ARG.patch_average==1
% [DATA_full2, ~,NOISE, Component_threshold] =subfunction_loop_for_NVR_avg(KSP2a,ARG.kernel_size(3),ARG.kernel_size(2),ARG.kernel_size(1),lambda,1,ARG.soft_thrs);
[DATA_full2, KSP2_weight] =subfunction_loop_for_NVR_avg(KSP2a,ARG.kernel_size(3),ARG.kernel_size(2),ARG.kernel_size(1),lambda,1,ARG.soft_thrs,KSP2_weight);
else
KSP2_weight_tmp =KSP2_weight([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
NOISE_tmp =NOISE([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
Component_threshold_tmp =Component_threshold([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
energy_removed_tmp =energy_removed([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
SNR_weight_tmp =SNR_weight([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
[DATA_full2,KSP2_weight_tmp,NOISE_tmp, Component_threshold_tmp,energy_removed_tmp,SNR_weight_tmp] =...
subfunction_loop_for_NVR_avg_update(KSP2a,ARG.kernel_size(3),ARG.kernel_size(2),ARG.kernel_size(1),lambda,1,ARG.soft_thrs,KSP2_weight_tmp,ARG,NOISE_tmp,Component_threshold_tmp,energy_removed_tmp,SNR_weight_tmp);
KSP2_weight([1:ARG.kernel_size(1)]+(n1-1),:,:,:)=KSP2_weight_tmp;
try; NOISE([1:ARG.kernel_size(1)]+(n1-1),:,:,:) =NOISE_tmp; catch;end
Component_threshold([1:ARG.kernel_size(1)]+(n1-1),:,:,:) = Component_threshold_tmp;
energy_removed([1:ARG.kernel_size(1)]+(n1-1),:,:,:) = energy_removed_tmp;
SNR_weight([1:ARG.kernel_size(1)]+(n1-1),:,:,:) = SNR_weight_tmp;
%DATA_full=subfunction_loop_for_NVR(KSP2a,ARG.kernel_size(3),ARG.kernel_size(2),ARG.kernel_size(1),lambda);
%DATA_full2(1, round(w2/2)+[1:size(DATA_full,1)],:,: )=DATA_full; % center plane only
end
end
end
if master==0
if QQ.KSP_processed(1,n1)~=2
save([ARG.filename 'slice' num2str(n1) '.mat'],'DATA_full2', '-v7.3' )
QQ.KSP_processed(1,n1)=2 ; % COMPLETED
end
else
if ARG.patch_average==1
tmp=KSP_recon([1:ARG.kernel_size(1)]+(n1-1),:,:,:) ;
KSP_recon([1:ARG.kernel_size(1)]+(n1-1),:,:,:)= tmp + DATA_full2;
else
KSP_recon([1:ARG.kernel_size(1)]+(n1-1) ,1:size(DATA_full2,2),:,:)= KSP_recon([1:ARG.kernel_size(1)]+(n1-1) ,1:size(DATA_full2,2),:,:) + DATA_full2;
end
QQ.KSP_processed(1,n1)=3 ;
end
end
return
function [KSP2_tmp_update, KSP2_weight]=subfunction_loop_for_NVR_avg(KSP2a,w3,w2,w1,lambda2,patch_avg, soft_thrs,KSP2_weight,ARG)
if ~exist('patch_avg'); patch_avg=1;end
if ~exist('soft_thrs'); soft_thrs=[]; end
if ~exist('KSP2_weight')
KSP2_weight=zeros(size(KSP2a(:,:,:,1)));
elseif isempty(KSP2_weight)
KSP2_weight=zeros(size(KSP2a(:,:,:,1)));
end
if ~exist('KSP2_tmp_update')
KSP2_tmp_update=zeros(size(KSP2a(:,:,:,:)));
elseif isempty(KSP2_tmp_update)
KSP2_tmp_update=zeros(size(KSP2a(:,:,:,:)));
end
% KSP2_weight=zeros(size(KSP2a(:,:,:,1)));
% KSP2_tmp_update=zeros(size(KSP2a));
% for n2=1:size(KSP2a,2)-w2+1;
% for n3=1:size(KSP2a,3)-w3+1;
for n2=[1: max(1,floor(w2/ARG.patch_average_sub)):size(KSP2a,2)*1-w2+1 size(KSP2a,2)-w2+1];
for n3=[1: max(1,floor(w3/ARG.patch_average_sub)):size(KSP2a,3)*1-w3+1 size(KSP2a,3)-w3+1 ];
KSP2_tmp=KSP2a(:,[1:w2]+(n2-1),[1:w3]+(n3-1),:);
tmp1=reshape(KSP2_tmp,[],size(KSP2_tmp,4));
[U,S,V]=svd([(tmp1) ],'econ');
S=diag(S);
[idx]=sum(S<lambda2);
if isempty(soft_thrs)
S(S<lambda2)=0;
elseif soft_thrs==10 % USING MPPCA
% disp('test for zero entries')
Test_mat=sum(tmp1,2);
sum(Test_mat==0)
centering=0;
MM=size(tmp1,1);
NNN=size(tmp1,2);
R = min(MM, NNN);
scaling = (max(MM, NNN) - (0:R-centering-1)) / NNN;
scaling = scaling(:);
vals=S;
vals = (vals).^2 / NNN;
% First estimation of Sigma^2; Eq 1 from ISMRM presentation
csum = cumsum(vals(R-centering:-1:1)); cmean = csum(R-centering:-1:1)./(R-centering:-1:1)'; sigmasq_1 = cmean./scaling;
% Second estimation of Sigma^2; Eq 2 from ISMRM presentation
gamma = (MM - (0:R-centering-1)) / NNN;
rangeMP = 4*sqrt(gamma(:));
rangeData = vals(1:R-centering) - vals(R-centering);
sigmasq_2 = rangeData./rangeMP;
t = find(sigmasq_2 < sigmasq_1, 1);
S(t:end)=0;
else
S(max(1,end-floor(idx*soft_thrs)):end)=0;
end
tmp1=U*diag(S)*V';
tmp1=reshape(tmp1,size(KSP2_tmp));
if patch_avg==1
KSP2_tmp_update(:,[1:w2]+(n2-1),[1:w3]+(n3-1),:) =...
KSP2_tmp_update(:,[1:w2]+(n2-1),[1:w3]+(n3-1),:) +tmp1;
KSP2_weight(:,[1:w2]+(n2-1),[1:w3]+(n3-1),:) =...
KSP2_weight(:,[1:w2]+(n2-1),[1:w3]+(n3-1),:) +1;
else
KSP2_tmp_update(:,round(w2/2)+(n2-1),round(w3/2)+(n3-1),:) =...
KSP2_tmp_update(:,round(w2/2)+(n2-1),round(w3/2)+(n3-1),:) +tmp1(1,round(end/2),round(end/2),:);
KSP2_weight(:,round(w2/2)+(n2-1),round(w3/2)+(n3-1),:) =...
KSP2_weight(:,round(w2/2)+(n2-1),round(w3/2)+(n3-1),:) +1;
end
end
end
return
function [KSP2_tmp_update, KSP2_weight,NOISE,KSP2_tmp_update_threshold,energy_removed,SNR_weight]=subfunction_loop_for_NVR_avg_update(KSP2a,w3,w2,w1,lambda2,patch_avg, soft_thrs,KSP2_weight,ARG,NOISE,KSP2_tmp_update_threshold,energy_removed,SNR_weight)
if ~isfield(ARG,'patch_scale'); patch_scale=1; else; patch_scale=ARG.patch_scale;end
if ~exist('patch_avg'); patch_avg=1;end % patch_avg=0; means zero only
if ~exist('soft_thrs'); soft_thrs=[]; end
if ~exist('KSP2_weight')
KSP2_weight=zeros(size(KSP2a(:,:,:,1)));
elseif isempty(KSP2_weight)
KSP2_weight=zeros(size(KSP2a(:,:,:,1)));
end
if ~exist('NOISE_tmp')'% ~exist('NOISE_tmpKSP2_tmp_update')
NOISE_tmp=zeros(size(KSP2a(:,:,:,1)));
elseif isempty(KSP2_tmp_update)
NOISE_tmp=zeros(size(KSP2a(:,:,:,1)));
end
if ~exist('KSP2_tmp_update_threshold')